Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Bulk nanostructured materials from severe plastic deformation

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Table Of Integrals Series And Products

Mechanical properties of nanocrystalline materials

The points raised in Morawiec's commentary are considered carefully. The question of the shortest distance between two grain boundaries remains unresolved and requires further research.

https://royalsocietypublishing.org/doi/pdf/10.1098/rspa.2016.0011

Response to commentary by Morawiec

Phase field modelling is a technique in (computational) material science that utilises diffuse interface constructions to simulate the dynamics of microstructural evolution. To date, phase field modelling of crystalline interfaces has been guided mainly by phenomenology and symmetry considerations, rather than microscopic physics. The central equation of motion minimises a free energy with respect to the phase field, which is considered as a space and time dependent, coarse-grained, continuous degree of freedom of the system. However, it is neither clear how to interpret the phase field microscopically, nor how to derive the equation of motion from atomic interactions. Based on the (classical) density functional theory by Haymet and Oxtoby, we derive the phase field model by Allen and Cahn, which is commonly used for modelling crystalline interfaces. In the present article, we summarise the physical implications of the various observables and parameters as well as the underlying approximations.

Phase field modelling of interfaces from first principles

Methods of minimizing free energies directly

ERRATUM: Carbon vacancies in titanium carbide

The structure of the GaAs(001)-(2 × 4) surface has been the subject of considerable controversy. We have fitted tight-binding parameters to local density approximation (LDA) results. Using a linear scaling tight-binding method we have been able to model sufficiently large unit cells to investigate the energetics of dimer row kinking, which provides strong evidence to support the identification of the β phase with the trench dimer model. Having done so, we returned to LDA calculations to investigate the interaction of the important chemical beam epitaxial growth precursor tri-methyl-gallium with the surface, in order to identify both the mobile precursor structure and the final bonded structure.

Adrian P. Sutton

Papers

Response to commentary by Morawiec

Phase field modelling of interfaces from first principles

Methods of minimizing free energies directly

ERRATUM: Carbon vacancies in titanium carbide

Tight-binding and local density approximation studies of semiconductor surfaces and small organic adsorbates